Name: Antarcticimicrobium luteum 318-1
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 163904

Type strain:

Species: Antarcticimicrobium luteum

Strain Designation: 318-1

Culture col. no.: JCM 30927, KCTC 72105, KEMB 7306-525

Strain history: S.-S. Lee; KEMB, Kyonggi Univ., South Korea; 318-1.

NCBI tax ID(s): 2547397 (species)

Section

Antarcticimicrobium luteum 318-1 is a mesophilic, Gram-negative, rod-shaped bacterium that forms circular colonies and was isolated from Marine sediment at a depth of 15 m at Masan Bay.

colony-forming
Gram-negative
rod-shaped
mesophilic
16S sequence
Bacteria
genome sequence

Information on the name and the taxonomic classification. Name and taxonomic classification

	Last LPSN update	14-12-2023 (DD-MM-YYYY)
	Domain	"Bacteria"
	Phylum	*Pseudomonadota*
	Class	*Alphaproteobacteria*
	Order	*Rhodobacterales*
	Family	*Roseobacteraceae*
	Genus	*Antarcticimicrobium*
	Species	**Antarcticimicrobium luteum**
	Full Scientific Name (LPSN)	Antarcticimicrobium luteum (Kim et al. 2019) Zhang et al. 2020

Synonym

Ruegeria lutea

Information on morphological and physiological properties Morphology

[Ref.: #68009]	Gram stain	negative
[Ref.: #69480]	Gram stain	negative Confidence in %100

[Ref.: #68009]	Cell length	0.8-1.5 µm

[Ref.: #68009]	Cell width	0.8-1.0 µm

[Ref.: #68009]	Cell shape	rod-shaped

[Ref.: #68009]	Motility	no

[Ref.: #68009]	Colony color	ivory coloured
[Ref.: #68009]	Colony shape	circular
[Ref.: #68009]	Incubation period	3 days
[Ref.: #68009]	Cultivation medium used	Marine agar (MA)

Information on culture and growth conditions Culture and growth conditions

	Kind of temperature		Temperature
[Ref.: #67770]		growth	25 °C
[Ref.: #68009]		growth	20-37 °C
[Ref.: #68009]		optimum	30 °C
[Ref.: #68009]	no	growth	15 °C
[Ref.: #68009]	no	growth	40 °C

[Ref.: #67770]	Temperature range	mesophilic
[Ref.: #68009]	Temperature range	mesophilic
[Ref.: #68009]	Temperature range	psychrophilic
[Ref.: #68009]	Temperature range	thermophilic

	pH	Kind of pH		pH
[Ref.: #68009]			optimum	7
[Ref.: #68009]			growth	6.0-8.0

Information on physiology and metabolism Physiology and metabolism

[Ref.: #69480]	Ability of spore formation	no Confidence in %99.998
[Ref.: #69481]	Ability of spore formation	no Confidence in %100

	Salt	Tested relation		Salt conc.
[Ref.: #68009]	NaCl		growth	1.0-7.0	%(w/v)
[Ref.: #68009]	NaCl	no	growth	0	%(w/v)
[Ref.: #68009]	NaCl		optimum	2.0-3.0	%(w/v)

[Ref.: #67770]	Observation	quinones: Q-10
[Ref.: #68009]	Observation	Cells accumulate PHB with capsule and slime
[Ref.: #68009]	Observation	The predominant ubiquinone is Q-10
[Ref.: #68009]	Observation	The major polar lipids are phosphatidylcholine, phosphatidylglycerol, diphosphatidylglycerol, and two unidentified aminolipids and three unidentified phospholipids
[Ref.: #68009]	Observation	Both molybdenum and molybdophospolic reagents were observed

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #68009]	(R)-malic acid ChEBI	-	carbon source
[Ref.: #68009]	(S)-lactate ChEBI	+	carbon source
[Ref.: #68009]	(S)-malic acid ChEBI	+	carbon source
[Ref.: #68009]	2-hydroxybutyrate ChEBI	+	carbon source
[Ref.: #68009]	2-oxobutanoate ChEBI	-	carbon source
[Ref.: #68009]	2-oxoglutarate ChEBI	+	carbon source
[Ref.: #68009]	3-hydroxybutyrate ChEBI	+	carbon source
[Ref.: #68009]	3-O-methyl-D-glucose ChEBI	-	carbon source
[Ref.: #68009]	4-hydroxyphenylacetic acid ChEBI	-	carbon source
[Ref.: #68009]	acetic acid ChEBI	+	carbon source
[Ref.: #68009]	acetoacetate ChEBI	-	carbon source
[Ref.: #68009]	adipate ChEBI	-	assimilation
[Ref.: #68009]	alpha-D-glucose ChEBI	-	carbon source
[Ref.: #68009]	alpha-lactose ChEBI	-	carbon source
[Ref.: #68009]	amygdalin ChEBI	+	builds acid from
[Ref.: #68009]	amygdalin ChEBI	-	assimilation
[Ref.: #68009]	arbutin ChEBI	+	builds acid from
[Ref.: #68009]	bromosuccinate ChEBI	-	carbon source
[Ref.: #68009]	cellobiose ChEBI	+	builds acid from
[Ref.: #68009]	cellobiose ChEBI	-	carbon source
[Ref.: #68009]	citrate ChEBI	-	carbon source
[Ref.: #68009]	D-arabinose ChEBI	-	builds acid from
[Ref.: #68009]	D-arabitol ChEBI	-	builds acid from
[Ref.: #68009]	D-arabitol ChEBI	+	carbon source
[Ref.: #68009]	D-aspartate ChEBI	-	carbon source
[Ref.: #68009]	D-fructose ChEBI	+/-	builds acid from
[Ref.: #68009]	D-fructose ChEBI	-	carbon source
[Ref.: #68009]	D-fructose 6-phosphate ChEBI	-	carbon source
[Ref.: #68009]	D-fucose ChEBI	+	builds acid from
[Ref.: #68009]	D-fucose ChEBI	+	carbon source
[Ref.: #68009]	D-galactose ChEBI	-	builds acid from
[Ref.: #68009]	D-galactose ChEBI	-	carbon source
[Ref.: #68009]	D-galacturonic acid ChEBI	+	carbon source
[Ref.: #68009]	D-glucarate ChEBI	-	carbon source
[Ref.: #68009]	D-gluconate ChEBI	+	carbon source
[Ref.: #68009]	D-glucose ChEBI	-	assimilation
[Ref.: #68009]	D-glucose ChEBI	-	builds acid from
[Ref.: #68009]	D-glucose 6-phosphate ChEBI	-	carbon source
[Ref.: #68009]	D-glucuronate ChEBI	+	carbon source
[Ref.: #68009]	D-lyxose ChEBI	-	builds acid from
[Ref.: #68009]	D-mannitol ChEBI	+/-	assimilation
[Ref.: #68009]	D-mannitol ChEBI	+/-	builds acid from
[Ref.: #68009]	D-mannitol ChEBI	+	assimilation
[Ref.: #68009]	D-mannitol ChEBI	+	carbon source
[Ref.: #68009]	D-mannose ChEBI	+	assimilation
[Ref.: #68009]	D-mannose ChEBI	+	builds acid from
[Ref.: #68009]	D-mannose ChEBI	-	carbon source
[Ref.: #68009]	D-ribose ChEBI	-	builds acid from
[Ref.: #68009]	D-serine ChEBI	-	carbon source
[Ref.: #68009]	D-sorbitol ChEBI	-	builds acid from
[Ref.: #68009]	D-sorbitol ChEBI	-	carbon source
[Ref.: #68009]	D-tagatose ChEBI	+	builds acid from
[Ref.: #68009]	D-trehalose ChEBI	-	carbon source
[Ref.: #68009]	D-xylose ChEBI	-	builds acid from
[Ref.: #68009]	decanoate ChEBI	-	assimilation
[Ref.: #68009]	erythritol ChEBI	-	builds acid from
[Ref.: #68009]	esculin ferric citrate	+	builds acid from
[Ref.: #68009]	ferric citrate ChEBI	-	assimilation
[Ref.: #68009]	formate ChEBI	+	carbon source
[Ref.: #68009]	galactarate ChEBI	-	carbon source
[Ref.: #68009]	galactitol ChEBI	-	builds acid from
[Ref.: #68009]	gamma-aminobutyric acid ChEBI	-	carbon source
[Ref.: #68009]	gelatin ChEBI	-	carbon source
[Ref.: #68009]	gentiobiose ChEBI	+	builds acid from
[Ref.: #68009]	gentiobiose ChEBI	-	carbon source
[Ref.: #68009]	glucuronamide ChEBI	+	carbon source
[Ref.: #68009]	glycerol ChEBI	-	builds acid from
[Ref.: #68009]	glycerol ChEBI	+	carbon source
[Ref.: #68009]	glycine-proline ChEBI	-	carbon source
[Ref.: #68009]	glycogen ChEBI	+	builds acid from
[Ref.: #68009]	inosine ChEBI	-	carbon source
[Ref.: #68009]	inulin ChEBI	+	builds acid from
[Ref.: #68009]	L-alanine ChEBI	-	carbon source
[Ref.: #68009]	L-arabinose ChEBI	-	builds acid from
[Ref.: #68009]	L-arabinose ChEBI	-	assimilation
[Ref.: #68009]	L-arabitol ChEBI	-	builds acid from
[Ref.: #68009]	L-arginine ChEBI	-	carbon source
[Ref.: #68009]	L-aspartate ChEBI	-	carbon source
[Ref.: #68009]	L-fucose ChEBI	+/-	builds acid from
[Ref.: #68009]	L-fucose ChEBI	+/-	carbon source
[Ref.: #68009]	L-galactonic acid gamma-lactone ChEBI	+	carbon source
[Ref.: #68009]	L-glutamate ChEBI	-	carbon source
[Ref.: #68009]	L-histidine ChEBI	-	carbon source
[Ref.: #68009]	L-pyroglutamate ChEBI	+	carbon source
[Ref.: #68009]	L-rhamnose ChEBI	-	builds acid from
[Ref.: #68009]	L-rhamnose ChEBI	+	assimilation
[Ref.: #68009]	L-rhamnose ChEBI	-	carbon source
[Ref.: #68009]	L-serine ChEBI	-	carbon source
[Ref.: #68009]	L-sorbose ChEBI	-	builds acid from
[Ref.: #68009]	L-tryptophan ChEBI	+	assimilation
[Ref.: #68009]	L-xylose ChEBI	-	builds acid from
[Ref.: #68009]	lactose ChEBI	+/-	builds acid from
[Ref.: #68009]	malate ChEBI	-	assimilation
[Ref.: #68009]	maltose ChEBI	-	assimilation
[Ref.: #68009]	maltose ChEBI	-	builds acid from
[Ref.: #68009]	maltose ChEBI	-	carbon source
[Ref.: #68009]	melezitose ChEBI	-	builds acid from
[Ref.: #68009]	melibiose ChEBI	-	builds acid from
[Ref.: #68009]	melibiose ChEBI	+	assimilation
[Ref.: #68009]	melibiose ChEBI	-	carbon source
[Ref.: #68009]	methyl (R)-lactate ChEBI	-	carbon source
[Ref.: #68009]	methyl alpha-D-glucopyranoside ChEBI	-	builds acid from
[Ref.: #68009]	methyl alpha-D-mannoside ChEBI	+	builds acid from
[Ref.: #68009]	methyl beta-D-glucopyranoside ChEBI	-	carbon source
[Ref.: #68009]	methyl beta-D-xylopyranoside ChEBI	+	builds acid from
[Ref.: #68009]	methyl pyruvate ChEBI	+	carbon source
[Ref.: #68009]	myo-inositol ChEBI	-	builds acid from
[Ref.: #68009]	myo-inositol ChEBI	+	assimilation
[Ref.: #68009]	myo-inositol ChEBI	-	carbon source
[Ref.: #68009]	N-acetyl-D-mannosamine ChEBI	-	carbon source
[Ref.: #68009]	N-acetylgalactosamine ChEBI	-	carbon source
[Ref.: #68009]	N-acetylglucosamine ChEBI	+	assimilation
[Ref.: #68009]	N-acetylglucosamine ChEBI	+	builds acid from
[Ref.: #68009]	N-acetylglucosamine ChEBI	-	carbon source
[Ref.: #68009]	n-acetylneuraminate ChEBI	-	carbon source
[Ref.: #68009]	nitrate ChEBI	+	reduction
[Ref.: #68009]	pectin ChEBI	-	carbon source
[Ref.: #68009]	phenylacetate ChEBI	-	assimilation
[Ref.: #68009]	potassium 2-dehydro-D-gluconate	-	builds acid from
[Ref.: #68009]	potassium 5-dehydro-D-gluconate	+	builds acid from
[Ref.: #68009]	potassium gluconate ChEBI	-	assimilation
[Ref.: #68009]	potassium gluconate ChEBI	-	builds acid from
[Ref.: #68009]	propionate ChEBI	+	carbon source
[Ref.: #68009]	quinate ChEBI	+	carbon source
[Ref.: #68009]	raffinose ChEBI	+	builds acid from
[Ref.: #68009]	raffinose ChEBI	-	carbon source
[Ref.: #68009]	ribitol ChEBI	-	builds acid from
[Ref.: #68009]	salicin ChEBI	+	builds acid from
[Ref.: #68009]	salicin ChEBI	-	carbon source
[Ref.: #68009]	sodium citrate ChEBI	-	assimilation
[Ref.: #68009]	sodium thiosulfate ChEBI	-	assimilation
[Ref.: #68009]	stachyose ChEBI	-	carbon source
[Ref.: #68009]	starch ChEBI	-	builds acid from
[Ref.: #68009]	sucrose ChEBI	-	builds acid from
[Ref.: #68009]	sucrose ChEBI	+	assimilation
[Ref.: #68009]	sucrose ChEBI	-	carbon source
[Ref.: #68009]	trehalose ChEBI	-	builds acid from
[Ref.: #68009]	turanose ChEBI	-	builds acid from
[Ref.: #68009]	turanose ChEBI	-	carbon source
[Ref.: #68009]	tween 40 ChEBI	-	carbon source
[Ref.: #68009]	urea ChEBI	-	assimilation
[Ref.: #68009]	xylitol ChEBI	-	builds acid from
	Only first 10 entries are displayed. Click here to see all.

	Enzyme	Enzyme activity	EC number
[Ref.: #68009]	acid phosphatase	+	3.1.3.2
[Ref.: #68009]	alkaline phosphatase	+	3.1.3.1
[Ref.: #68009]	alpha-chymotrypsin	-	3.4.21.1
[Ref.: #68009]	alpha-fucosidase	-	3.2.1.51
[Ref.: #68009]	alpha-galactosidase	-	3.2.1.22
[Ref.: #68009]	alpha-glucosidase	-	3.2.1.20
[Ref.: #68009]	alpha-mannosidase	-	3.2.1.24
[Ref.: #68009]	arginine dihydrolase	-	3.5.3.6
[Ref.: #68009]	beta-galactosidase	-	3.2.1.23
[Ref.: #68009]	beta-glucosidase	-	3.2.1.21
[Ref.: #68009]	beta-glucuronidase	-	3.2.1.31
[Ref.: #68009]	catalase	+	1.11.1.6
[Ref.: #68009]	cystine arylamidase	+	3.4.11.3
[Ref.: #68009]	cytochrome oxidase	+	1.9.3.1
[Ref.: #68009]	esterase (C 4)	+
[Ref.: #68009]	esterase Lipase (C 8)	+
[Ref.: #68009]	leucine arylamidase	+	3.4.11.1
[Ref.: #68009]	lipase (C 14)	+
[Ref.: #68009]	lysine decarboxylase	-	4.1.1.18
[Ref.: #68009]	N-acetyl-beta-glucosaminidase	-	3.2.1.52
[Ref.: #68009]	naphthol-AS-BI-phosphohydrolase	+
[Ref.: #68009]	ornithine decarboxylase	-	4.1.1.17
[Ref.: #68009]	trypsin	-	3.4.21.4
[Ref.: #68009]	valine arylamidase	+
	Only first 10 entries are displayed. Click here to see all.

Information on isolation source, the sampling and environmental conditions Isolation, sampling and environmental information

[Ref.: #67770]	Sample type/isolated from	Marine sediment at a depth of 15 m at Masan Bay
[Ref.: #67770]	Geographic location (country and/or sea, region)	Gyeongsangnam-do
[Ref.: #67770]	Country	Republic of Korea
[Ref.: #67770]	Country ISO 3 Code	KOR
[Ref.: #67770]	Continent	Asia

[Ref.: #68009]	Sample type/isolated from	marine sediment at a depth of 15m at Masan Bay
[Ref.: #68009]	Geographic location (country and/or sea, region)	Gyeongsangnam-do
[Ref.: #68009]	Country	Republic of Korea
[Ref.: #68009]	Country ISO 3 Code	KOR
[Ref.: #68009]	Continent	Asia
[Ref.: #68009]	Geographic location	35.1036°/128.6040°
* marker position based on {}

[Ref.: #69479]

Global distribution of 16S sequence MK246204 (>99% sequence identity) for Antarcticimicrobium luteum from Microbeatlas

Aquatic Samples	725
Soil Samples	19
Animal Samples	182
Plant Samples	12
Total Samples	938

Information on genomic background e.g. entries in nucleic sequence databass Sequence information

16S Sequence information:

	Sequence accession description	Seq. accession number	Sequence length (bp)	Sequence database	Associated NCBI tax ID
[Ref.: #68009]	Ruegeria sp. strain 318-1 16S ribosomal RNA gene, partial sequence	MK246204	1420	ENA	2547397 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #67770]	Antarcticimicrobium luteum 318-1	GCA_004358185	contig	GenBank	2547397 tax ID
[Ref.: #66792]	Ruegeria sp. 318-1	2547397.3	wgs	PATRIC	2547397 tax ID	*

[Ref.: #68009]

GC-content

65.75 mol%

genome sequence analysis

Data predicted using genome information as a basis Genome-based predictions

	Trait	Prediction	Confidence in %	In training data
	Predictions from GenomeNet Sporulation v. 1 based on: Ruegeria sp. 318-1 PATRIC: 2547397.3
[Ref.: #69481]	spore-forming	no	100	no

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Ruegeria sp. 318-1 PATRIC: 2547397.3
[Ref.: #69480]	motile	no	52.456	no
[Ref.: #69480]	gram-positive	no	97.898	no
[Ref.: #69480]	anaerobic	no	98.514	no
[Ref.: #69480]	aerobic	yes	87.14	no
[Ref.: #69480]	halophile	yes	74.354	no
[Ref.: #69480]	spore-forming	no	95.6	no
[Ref.: #69480]	glucose-util	yes	54.173	yes
[Ref.: #69480]	flagellated	no	88.494	no
[Ref.: #69480]	thermophile	no	96.651	no
[Ref.: #69480]	glucose-ferment	no	90.676	no

Availability in culture collections External links

[Ref.: #67770]

Culture collection no.

JCM 30927, KCTC 72105, KEMB 7306-525

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Antarcticimicrobium sediminis gen. nov., sp. nov., isolated from Antarctic intertidal sediment, transfer of Ruegeria lutea to Antarcticimicrobium gen. nov. as Antarcticimicrobium luteum comb. nov.	Zhang S, Liu WX, Liu NH, He XY, Su HN, Li CY, Zhang YZ, Song XY, Zhang XY	Int J Syst Evol Microbiol	10.1099/ijsem.0.004083	2020	*
Phylogeny	Ruegeria lutea sp. nov., isolated from marine sediment, Masan Bay, South Korea.	Kim J, Kim DY, Yang KH, Kim S, Lee SS	Int J Syst Evol Microbiol	10.1099/ijsem.0.003568	2019	*

References

#20215

Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M.: List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ. IJSEM ( DOI 10.1099/ijsem.0.004332 )

#66792

Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann: Automatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) .

#67770 Japan Collection of Microorganism (JCM) ; Curators of the JCM;

#68009

Jinsoo Kim, Da-Young Kim, Keun-Hyeok Yan, Sungchul Kim, Sang-Seob Lee: Ruegeria lutea sp. nov., isolated from marine sediment, Masan Bay, South Korea. IJSEM 69: 2854 - 2861 2019 ( DOI 10.1099/ijsem.0.003568 )

#69479

João F Matias Rodrigues, Janko Tackmann,Gregor Rot, Thomas SB Schmidt, Lukas Malfertheiner, Mihai Danaila,Marija Dmitrijeva, Daniela Gaio, Nicolas Näpflin and Christian von Mering. University of Zurich.: MicrobeAtlas 1.0 beta .

#69480

Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann: Predictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) .

#69481

Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch: Predictions based on the model GenomeNet Sporulation v. 1 . ( DOI 10.21203/rs.3.rs-2527258/v1 )

* These data were automatically processed and therefore are not curated

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Search for species Antarcticimicrobium luteum in external resources:
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Ruegeria sp. 318-1

Ruegeria sp. 318-1

Change proposal

Change proposal